Variant report

Variant	rs11075059
Chromosome Location	chr16:12383329-12383330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:12359512..12361860-chr16:12382352..12385228,2	MCF-7	breast:
2	chr16:12289297..12291901-chr16:12382629..12384781,2	MCF-7	breast:
3	chr16:12381810..12383489-chr16:12387831..12390561,2	MCF-7	breast:
4	chr16:12352461..12354731-chr16:12381586..12384125,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11075057	0.82[EUR][1000 genomes]
rs11075058	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11075062	0.86[GIH][hapmap]
rs11639640	0.86[EUR][1000 genomes]
rs11644788	0.87[EUR][1000 genomes]
rs11648255	0.80[EUR][1000 genomes]
rs11649626	0.86[EUR][1000 genomes]
rs11861914	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12148953	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12445263	0.91[EUR][1000 genomes]
rs12445569	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12446650	0.91[EUR][1000 genomes]
rs12448443	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13335852	0.87[EUR][1000 genomes]
rs176717	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17697005	0.91[EUR][1000 genomes]
rs17764604	0.91[EUR][1000 genomes]
rs2089251	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs209846	0.81[EUR][1000 genomes]
rs209849	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209850	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209851	0.87[EUR][1000 genomes]
rs209853	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209855	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209856	0.88[EUR][1000 genomes]
rs2856771	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35818743	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4305040	0.85[EUR][1000 genomes]
rs4780417	0.89[EUR][1000 genomes]
rs4780418	0.91[EUR][1000 genomes]
rs4780419	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4781200	0.91[EUR][1000 genomes]
rs4781201	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4781202	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4781209	0.81[CEU][hapmap];0.85[GIH][hapmap]
rs4781214	0.89[GIH][hapmap]
rs6498274	0.84[EUR][1000 genomes]
rs7184477	0.81[EUR][1000 genomes]
rs7189386	0.90[EUR][1000 genomes]
rs7189945	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7190509	0.81[CEU][hapmap];0.85[GIH][hapmap]
rs7191442	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7192102	0.90[EUR][1000 genomes]
rs7194718	0.86[EUR][1000 genomes]
rs7194981	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195520	0.81[EUR][1000 genomes]
rs7197417	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7199556	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7200289	0.84[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs7201621	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7204209	0.92[EUR][1000 genomes]
rs7204333	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7500910	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8046012	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8051758	0.84[EUR][1000 genomes]
rs8058876	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8061549	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8063991	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs868773	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs869289	0.87[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs905950	0.87[EUR][1000 genomes]
rs9284322	0.88[GIH][hapmap]
rs9630612	0.87[EUR][1000 genomes]
rs9921728	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9927705	0.88[EUR][1000 genomes]
rs9928214	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9930625	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9937220	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv457411	chr16:12363304-12520199	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv571462	chr16:12363304-12520199	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1045385	chr16:12376389-12517006	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542748	chr16:12376389-12517006	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11075059	C16orf63	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12323400-12394200	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr16:12338200-12396200	Weak transcription	Thymus	Thymus
3	chr16:12347800-12395200	Weak transcription	Right Ventricle	heart
4	chr16:12356000-12390200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr16:12359800-12418000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr16:12365200-12388000	Weak transcription	Pancreas	Pancrea
7	chr16:12365200-12388400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr16:12366400-12384000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr16:12370400-12383600	Weak transcription	Colon Smooth Muscle	Colon
10	chr16:12371400-12456800	Weak transcription	Aorta	Aorta
11	chr16:12372800-12393800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr16:12373000-12384200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr16:12373200-12383800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr16:12373400-12414200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr16:12373600-12396600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr16:12374000-12389400	Weak transcription	HSMMtube	muscle
17	chr16:12374000-12397400	Weak transcription	Ovary	ovary
18	chr16:12374200-12384600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr16:12374200-12417200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr16:12375600-12384000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr16:12375600-12386400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr16:12375800-12383800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr16:12378200-12384200	Weak transcription	Adipose Nuclei	Adipose
24	chr16:12378600-12388400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr16:12379200-12385200	Weak transcription	Fetal Brain Male	brain
26	chr16:12379200-12388400	Weak transcription	Right Atrium	heart
27	chr16:12380600-12384800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr16:12381000-12385000	Strong transcription	Primary B cells from cord blood	blood
29	chr16:12381400-12384600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr16:12381800-12383400	Strong transcription	GM12878-XiMat	blood
31	chr16:12381800-12384200	Enhancers	Spleen	Spleen
32	chr16:12382000-12384400	Enhancers	Duodenum Mucosa	Duodenum
33	chr16:12382000-12386200	Strong transcription	Primary T cells from cord blood	blood
34	chr16:12382600-12383600	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr16:12382600-12384200	Enhancers	Placenta	Placenta
36	chr16:12382600-12384400	Flanking Active TSS	HepG2	liver
37	chr16:12382800-12383800	Enhancers	Left Ventricle	heart
38	chr16:12382800-12384200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr16:12382800-12384200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr16:12382800-12384400	Enhancers	Fetal Intestine Small	intestine
41	chr16:12382800-12384400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr16:12383000-12383400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr16:12383000-12383400	Enhancers	Fetal Brain Female	brain
44	chr16:12383000-12383800	Enhancers	Fetal Muscle Leg	muscle
45	chr16:12383000-12384000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
46	chr16:12383000-12384000	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr16:12383000-12384000	Enhancers	Esophagus	oesophagus
48	chr16:12383000-12384000	Enhancers	Lung	lung
49	chr16:12383000-12384200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr16:12383000-12384200	Enhancers	Fetal Intestine Large	intestine

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